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Nature. Author manuscript; available in PMC 2016 November 18.
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Published in final edited form as:

Nature. ; 535(7610): 85–93. doi:10.1038/nature18849.

Interactions between the microbiota and pathogenic bacteria in

the gut
Andreas J. Bäumler1 and Vanessa Sperandio2,3
1Department of Medical Microbiology and Immunology, University of California, Davis, School of
Medicine, Davis, California 95616, USA
2Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas
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75390-9048, USA
3Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas
75390-9038, USA

Abstract
The microbiome has an important role in human health. Changes in the microbiota can confer
resistance to or promote infection by pathogenic bacteria. Antibiotics have a profound impact on
the microbiota that alters the nutritional landscape of the gut and can lead to the expansion of
pathogenic populations. Pathogenic bacteria exploit microbiota-derived sources of carbon and
nitrogen as nutrients and regulatory signals to promote their own growth and virulence. By
eliciting inflammation, these bacteria alter the intestinal environment and use unique systems for
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respiration and metal acquisition to drive their expansion. Unravelling the interactions between the
microbiota, the host and pathogenic bacteria will produce strategies for manipulating the
microbiota against infectious diseases.

Appreciation of the important role of the microbiota in human health and nutrition has
grown steadily in the past decade. Initial studies focused on cataloguing the microbial
species that comprise the microbiota and correlating the composition of the microbiota with
the health or disease state of the host. The present period of renaissance has resulted in
technologies and interdisciplinary research that are conducive to mechanistic studies and, in
particular, those that focus on associations between the microbiota, the host and pathogenic
bacteria. Exciting research is now starting to unravel how the composition of the microbiota
can offer either resistance or assistance to invading pathogenic species. The majority of these
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studies were conducted in the gastrointestinal tract, in which associations between the host
and microbes are of paramount importance. The gut microbiota of each individual is unique
at the genus and species levels; however, it is more generally conserved at the phylum level,
which is populated most prominently by Bacteroidetes and Firmicutes, followed by
Proteobacteria and Actinobacteria. Host genetics, diet and environmental insults such as

Reprints and permissions information is available at www.nature.com/reprints.

Correspondence should be addressed to V.S. (vanessa.sperandio@utsouthwestern.edu).
The authors declare no competing financial interests.
Readers are welcome to comment on the online version of this paper at go.nature.com/28ix4vg.
 Bäumler and Sperandio Page 2

treatment with antibiotics alter the microbiota1–4, which can lead to varying susceptibility to
infectious diseases between individuals5.
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The microbiota can promote resistance to colonization by pathogenic species6–9. For

instance, mice that are treated with antibiotics or that are bred in sterile environments
(known as germ-free mice) are more susceptible to enteric pathogenic bacteria such as
Shigella flexneri, Citrobacter rodentium, Listeria monocytogenes and Salmonella enterica
serovar Typhimurium10–13. And some microbiotas can lead to the expansion or enhanced
virulence of pathogenic populations7. A notable example concerns how differences in the
composition of microbiotas determine the susceptibility of the mice to infection with C.
rodentium: the transplantation of microbiotas from strains of mice that are susceptible to
infection induced similar susceptibility in animals that were previously insusceptible, and
the transplantation of microbiotas from resistant animals led to resistance to infection in
previously susceptible animals14,15. Epidemiological surveys reinforce this idea. For
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example, differential susceptibility to infection with Campylobacter jejuni was shown to

depend on the species composition of the microbiotas in a study of Swedish adults16.
Individuals with a higher diversity within their microbiotas, and with an abundance of
bacteria from the genera Dorea and Coprococcus, were significantly recalcitrant to C. jejuni
infection compared with people who had low-diversity microbiotas and non-abundance of
Dorea and Coprococcus.

The host’s diet profoundly affects the composition of the microbiota, with repercussions for
the physiology, immunity and susceptibility to infectious diseases of the host17. Dietary
choices have been shown to affect colonization by enterohaemorrhagic Escherichia coli
(EHEC) serotype O157:H7 and the severity and length of its resulting disease18, and
supplementation of the diet with phytonutrients promotes the expansion of beneficial
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Clostridia species that protect mice from colonization by C. rodentium19.

The use of innovative technologies, in combination with more conventional approaches, is

driving our understanding of the interactions between the microbiota, the host and
pathogenic bacteria. The genetic tractability of several species of bacteria, as well as of their
mammalian hosts (such as mice), allows for the mechanistic investigation of these
relationships. The investigation of changes in the composition of microbiotas has been
driven by next-generation sequencing, which also facilitated the analysis of transcriptomes.
The growing power and finesse of metabolomics studies are quickly expanding our
knowledge of the impact of both the microbiota and of pathogenic bacteria on the metabolic
landscape of the gut. Here, we review advances in our understanding of the complex
relationships that determine the severity and outcome of gastrointestinal infections. The
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majority of the mechanistic studies that investigate these interactions have been conducted in
S. Typhimurium, EHEC and Clostridium difficile: therefore, these pathogenic organisms are
covered more extensively than others in this Review.

Antibiotics
Antibiotics revolutionized medicine and were justifiably dubbed ‘magic bullets’ against
bacterial infections. However, conventional antibiotics are generally bacteriostatic or

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bactericidal, which means that they indiscriminately kill or prevent the growth of both
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pathogenic and beneficial microbes. Antibiotics can alter the taxonomic, genomic and
functional features of the microbiota, and their effects can be rapid and sometimes
everlasting20. They can decrease the diversity of the microbiota, which compromises
resistance to colonization by incoming pathogenic bacteria20 — most notably leading to an
expansion of C. difficile that can cause diarrhoea that leads to potentially fatal colitis21.

C. difficile is a spore-forming bacterium that, on germination, colonizes the large intestine

and causes colitis through the action of two toxins: TcdA and TcdB. The majority of C.
difficile infections are nosocomial, but there has also been an increase in community-
acquired infections, mainly due to the ubiquitous presence of C. difficile spores. C. difficile
can colonize the mammalian intestine without causing disease, but one of the most important
risk factors for colitis that is mediated by C. difficile is the use of antibiotics21. The
antibiotics-mediated loss of resistance to colonization also allows colonization by S.
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Typhimurium and the development of disease22. Both C. difficile and S. Typhimurium

catabolize sialic acid as a source of carbon in the lumen to promote their expansion23. They
rely on saccharolytic members of the microbiota, such as Bacteroides thetaiotaomicron, to
make this sugar freely available in the intestinal lumen. Treatment with antibiotics increases
the abundance of host-derived free sialic acid as well as enhancing its release into the lumen
by B. thetaiotaomicron, which promotes the expansion of the two pathogenic bacteria23.
Antibiotic use also triggers production of the organic acid succinate, another microbiota-
derived nutrient that confers a growth advantage to C. difficile. It is often present at a low
concentration in the microbiotas of conventional mice, but its presence increases on
treatment with antibiotics, which promotes a bloom of C. difficile24 (Fig. 1).

Knowledge of how microbiota disruption affects the ability of bona fide or opportunistic
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pathogenic organisms to infect hosts is still in its infancy. However, two underlying themes
converge: microbiota-induced changes in the metabolite landscape of the gut and
inflammation.

Utilization of nutrients
Simple dietary sugars are absorbed in the small intestine, which means that they are
unavailable as sources of carbon for the microbiota and pathogenic bacteria in the colon. The
most abundant members of the microbiota are those that are able to utilize the undigested
plant polysaccharides and host glycans that are present in the colon25.

The gut epithelium is protected by a layer of mucus that is composed of proteins known as
mucins that are rich in fucose, galactose, sialic acid, N-acetylgalactosamine, N-
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acetylglucosamine and mannose. These sugars are harvested by saccharolytic members of

the microbiota, such as Bacteroidales in the gut, which makes them available to species
within the microbiota that lack this capability26. However, pathogenic bacteria in the gut can
also exploit the availability of these sugars to promote their own expansion. Several studies
have used B. thetaiotaomicron as a model Bacteroides in which to investigate these
syntrophic links. Sialic acid is a terminal sugar of some mucosal glycans, and B.
thetaiotaomicron has sialidase activity but lacks the catabolic pathway for sialic-acid

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utilization. The bacterium therefore releases sialic acid to gain access to underlying glycans
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that it can use as a source of carbon. The sialic acid that B. thetaiotaomicron releases from
the mucus can be catabolized by both C. difficile and S. Typhimurium, which provides them
with a growth advantage23. The ability of the microbiota to use sialic acid therefore depends
on the action of B. thetaiotaomicron, and mutants that lack sialidase fail to enhance the
growth of these two pathogenic bacteria23.

B. thetaiotaomicron also releases fucose from the mucus. It harbours multiple enzymes that
can cleave fucose from host glycans, so its presence results in the high availability of fucose
in the lumen of the gut27–30. This free fucose can also be used as a source of carbon by S.
Typhimurium23. Importantly, B. thetaiotaomicron can promote the fucosylation of mucosal
glycans when introduced into monoassociated germ-free mice31,32.

The microbiota resides in the lumen and the outer mucus layer of the intestine. EHEC,
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however, aims to achieve a unique niche by closely adhering to the enterocytes of the
intestinal epithelium. To achieve its goal, EHEC must successfully compete with the
microbiota for nutrients. B. thetaiotaomicron does not need to compete with EHEC,
however, because it can utilize polysaccharides; EHEC can only utilize monosaccharides
and disaccharides13,33. EHEC’s main competitors are commensal E. coli, which
preferentially utilizes fucose as a source of carbon when growing in the mammalian
intestine13,33. To circumvent this competition, EHEC utilizes other sources of sugar, such as
galactose, the hexuranates, mannose and ribose, which commensal E. coli cannot catabolize
optimally33,34 (Fig. 2).

EHEC uses fucose as a signalling molecule with which to adjust its metabolism and to
regulate the expression of its virulence repertoire in the lumen and the outer mucus layer of
the colon35. It horizontally acquired a pathogenicity island of genes that encode a fucose-
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sensing signalling-transduction system35. This system is unique to EHEC and to C.

rodentium35 (which is used extensively in mouse models as a surrogate for the human
pathogen EHEC36). It is composed of the membrane-bound histidine sensor kinase FusK,
which specifically autophosphorylates in response to fucose. FusK then transfers its
phosphate to a response regulator called FusR, which is a transcription factor.
Phosphorylation activates FusR, which represses the expression of the fucose utilization
genes in EHEC, and helps EHEC to avoid the need to compete for this nutrient with
commensal E. coli35. To prevent the unnecessary expenditure of energy by EHEC, FusR
represses the genes that encode the EHEC virulence machinery, a syringe-like apparatus
known as a type III secretion system (T3SS), which the bacterium uses to adhere itself to
enterocytes and highjack the function of these host cells35. EHEC therefore uses fucose, a
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host-derived signal that is made available by the microbiota, to sense the environment of the
intestinal lumen and to modulate its own metabolism and virulence.

To reach the lining of the epithelium, EHEC and C. rodentium produce mucinases37, which
cleave the protein backbone of mucin-type glycoproteins. Expression of these enzymes is
increased by metabolites that are produced by B. thetaiotaomicron38. Because mucus is one
of the main sources of sugar in the colon, where EHEC and C. rodentium colonize,
obliteration of the mucus layer creates a nutrient-poor environment near the epithelium that

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is referred to as gluconeogenic. The colonization of mice by B. thetaiotaomicron therefore

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profoundly changes the metabolic landscape of the mouse gut because it raises the levels of
organic acids such as succinate24,38,39. Moreover, several metabolites that indicate a
gluconeogenic environment, such as lactate and glycerate, are also elevated38. EHEC and C.
rodentium sense this gluconeogenic and succinate-rich environment through the
transcriptional regulator Cra. On receiving the cue that they have reached the lining of the
gut epithelium, these bacteria activate the expression of their T3SSs38. EHEC therefore
exploits metabolic cues from B. thetaiotaomicron, and probably other members of the
microbiota, to precisely programme its metabolism and virulence (Fig. 2).

Other pathogenic bacteria can also adjust their gene expression in the presence of
microbiota-produced succinate. C. difficile induces a pathway that converts succinate to
butyrate, which confers a growth advantage in vivo24. Populations of C. difficile mutants
that are unable to convert succinate fail to expand in the gut in the presence of B.
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thetaiotaomicron24.

Several short-chain fatty acids that are produced by the microbiota, are important
determinants of interactions between the microbiota and pathogenic bacteria in the gut. The
abundance and composition of short-chain fatty acids is distinct in each compartment of the
intestine, and the ability to sense these differences might help pathogenic bacteria in niche
recognition. The most abundant short-chain fatty acids in the gut are acetate, propionate and
butyrate. S. Typhimurium preferably colonizes the ileum40, which generally contains acetate
at a concentration of 30 mM. This acetate concentration enhances the expression of the S.
Typhimurium Salmonella pathogenicity island 1 (SPI-1)-encoded T3SS (T3SS-1), which is
involved in the bacterium’s invasion of the host. Conversely, 70 mM propionate and 20 mM
butyrate, concentrations typical of the colon, suppress the expression of the T3SS-1 (ref. 41).
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Propionate and butyrate seem to affect the T3SS-1 regulatory cascade at various levels.
However, the detailed mechanism of this regulation is yet to be unravelled. In EHEC,
exposure to the levels of butyrate found in the colon increases the expression of the EHEC
T3SS through post-transcriptional activation of the transcriptional regulator Lrp42. Exposure
to the concentrations of acetate and propionate that are found in the small intestine does not
significantly affect the virulence of EHEC.

Diet has a profound effect on the composition of the microbiota and the concentration of
short-chain fatty acids in the gut17. A diet that is high in fibre results in the enhanced
production of butyrate by the gut microbiota. That increases the host’s expression of
globotriaosylceramide, which is a receptor for the Shiga toxin that is produced by EHEC18.
Shiga toxin can lead to the development of haemolytic uraemic syndrome (HUS) and is the
cause of the morbidity and mortality associated with outbreaks of EHEC43. Consequently,
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animals that are fed a high-fibre diet are more susceptible to Shiga toxin than are those on a
low-fibre diet and develop more severe disease18. Conversely, increased levels of
microbiota-derived acetate protect animals from disease that is caused by the toxin. Certain
species of Bifidobacteria contribute to higher levels of acetate in the gut, which helps to
improve the barrier function of the intestinal epithelium and to prevent Shiga toxin from
reaching the bloodstream44.

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Enteric pathogenic bacteria also use other nutrients to successfully overcome the
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microbiota’s resistance to their colonization. Ethanolamine is abundant in the mammalian

intestine45. It can be used as a source of carbon and of nitrogen by a number of pathogenic
species46, and food-borne bacteria are particularly adept at using it. However, it cannot be
metabolized by the majority of commensal species47. S. Typhimurium, EHEC and L.
monocytogenes gain a growth advantage in the intestine through their ability to use this
compound45,48,49. Ethanolamine is also used as a signal by EHEC and S. Typhimurium to
activate the expression of virulence genes50,51. And S. Typhimurium uses hydrogen
produced by the microbiota as an energy source to enhance its growth during the initial stage
of infection52.

The exploitation of microbiota-derived molecules as both nutrients and signals is crucial for
the successful infection of the host by pathogenic bacteria. Although such organisms have
clearly developed many strategies through which to circumvent the microbiota’s resistance
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to colonization, and in many cases even employ its help, the microbiota pushes back, which
creates an intense competition for resources. The ability of EHEC to colonize the intestine
stems from differences in the sources of sugar that are used by EHEC and by commensal E.
coli. For example, the presence of multiple strains of commensal E. coli with overlapping
nutritional requirements interferes with the colonization of the mouse intestine by EHEC53.
This study uses a streptomycin-treated mouse model of EHEC and three distinct commensal
strains of E. coli to assess differential sugar requirements for the successful colonization of
the intestines53. EHEC could colonize mice that were pre-colonized with any one of the
commensal strains, but it could not colonize mice that were pre-colonized with all three
strains53. EHEC has evolved to exploit distinct sources of sugar during colonization of the
gut. It utilizes catabolic pathways for the hexuronates glucuronate and galacturonate and for
sucrose that are not employed by commensal E. coli within the gut33,53. It can also
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metabolize several sugars simultaneously. The loss of multiple catabolic pathways has an
additive effect on colonization. This phenomenon is not observed in commensal E. coli,
however, which suggests that E. coli uses available sugars in a stepwise fashion54. EHEC
therefore differs from commensal E. coli in metabolic strategy and the use of nutrients for
the colonization of the mammalian intestine.

C. rodentium is outcompeted and then cleared from the mouse gut through a bloom in the
population of commensal E. coli, which competes with C. rodentium for monosaccharides
for nutrition13. By contrast, C. rodentium is not cleared by B. thetaiotaomicron in germ-free
mice that are fed a diet that contains both monosaccharides, which can be used by
Enterobacteriacae such as C. rodentium, and polysaccharides, which can be used by
Bacteroides. However, when the mice are switched to a diet that consists only of
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monosaccharides, B. thetaiotaomicron and C. rodentium are forced to compete for sugars,

and B. thetaiotaomicron outcompetes C. rodentium13. The ability of pathogenic bacteria to
successfully compete with commensal species for nutrients is therefore important for their
establishment in the gut.

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Interception of signals from the microbiota and the host

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The microbiota affects the risks and courses of enteric diseases. Vibrio cholerae is a major
cause of explosive diarrhoea in which there is extensive disruption of the intestinal
population of microbes. Metagenomic studies of the faecal microbiota of people with
cholera in Bangladesh show that recovery is characterized by a certain microbiota signature.
Reconstitution of this microbiota in germ-free mice restricts the infectivity of V. cholerae.
Specifically, the presence of Ruminococcus obeum can hamper the colonization of the
intestines by V. cholerae through the production of the furanone signal autoinducer-2, which
causes the repression of several V. cholerae colonization factors55.

Another example of the effect of microbiota-derived signals on host colonization is their use
by EHEC in the colonization of its ruminal reservoir. EHEC exclusively colonizes the recto–
anal junction of adult cattle. Through the sensor protein SdiA, EHEC detects acyl-
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homoserine lactone signals from the rumen microbiota, which it uses to reprogram itself to
survive the acidic pH of the animal’s stomachs and to successfully colonize the rectoanal
junction56.

As well as being able to directly detect signals that are derived from the microbiota,
pathogenic bacteria can detect host-derived signals that have been modified by the
microbiota to modulate their virulence. V. cholerae has a type VI secretion system (T6SS),
which it uses to kill other bacteria. During its colonization of the intestine, V. cholerae
comes in contact with the mucosal microbiota, which can affect the composition of bile
acids in the intestine. For example, Bifidobacterium bifidum negatively regulates the T6SS
activity of V. cholerae through the metabolic conversion of three bile acids
(glycodeoxycholic acid, taurodeoxycholic acid and cholic acid) into the bile acid
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deoxycholic acid. Deoxycholic acid, but not its unmodified salts, decreases the expression of
T6SS genes. This leads to a decrease in the killing of E. coli by V. cholerae owing to bile-
acid conversion by other commensals, which decreases the activity of the T6SS57.

Another microbiota-modified host signal that is detected by pathogenic bacteria is the

neurotransmitter noradrenaline. The gut is highly innervated, and neurotransmitters are
important signals in the gastrointestinal tract, where they modulate peristalsis, the flow of
blood and the secretion of ions58. The microbiota affects the availability of neurotransmitters
in the intestinal lumen, as well as their biosynthesis. For example, the microbiota induces
biosynthesis of serotonin59, and microbiota-derived enzymatic activities increase the levels
of active noradrenaline in the gut lumen60. Noradrenaline is synthesized by the adrenergic
neurons of the enteric nervous system61 and it is inactivated by the host through conjugation
with glucuronic acid (to produce a glucuronide). Microbiota-produced enzymes known as
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glucuronidases then deconjugate glucuronic acid from noradrenaline, which increases the
amount of active noradrenaline in the lumen of the intestine60. Several pathogenic bacteria
of the gut, including EHEC, S. Typhimurium and V. parahaemolyticus, sense noradrenaline
to activate the expression of virulence genes62–65. Two adrenergic sensors have been
identified in bacteria: the membrane-bound histidine kinases QseC and QseE66,67. QseC also
detects the microbiota-produced signal autoinducer-3 (refs 64 and 66), so the sensing of

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signals from both the host and the microbiota converge at the level of a single receptor, a
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process known as inter-kingdom signalling.

Inflammation
Although diet and the composition of the microbiota heavily influence the availability of
nutrients in the gut, the host also has an important part to play. A crucial driver of changes in
the gut environment is the inflammatory response of the host. Intestinal inflammation in
people is associated with an imbalance in the microbiota, known as dysbiosis, and is
characterized by a reduced diversity of microbes, a reduced abundance of obligate anaerobic
bacteria and an expansion of facultative anaerobic bacteria in the phylum Proteobacteria,
mostly members of the family Enterobacteriaceae68–73. Similar changes in the composition
of the gut microbiota are observed in mice with chemically induced colitis74 and genetically
induced colitis75. These changes in the structure of the microbiota probably reflect an altered
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nutritional environment that is created by the inflammatory response of the host.

The availability of nutrients in the large intestine is altered during inflammation through
changes in the composition of mucous carbohydrates. Interleukin (IL)-22, a cytokine that is
prominently induced in the intestinal mucosa when mice and rhesus macaques are infected
with S. Typhimurium76,77, stimulates the epithelial expression of galactoside 2-α-L-
fucosyltransferase 2 and enhances the α(1,2)-fucosylation of mucus carbohydrates78,79. The
gut microbiota can liberate fucose from mucus carbohydrates23,80, which leads to the
induction of genes for fucose utilization in E. coli78. Similarly, increased fucosylation of
glycans is observed during S. Typhimurium-induced colitis in mice, which correlates with
elevated synthesis of the proteins involved in fucose utilization81. Mucus fucosylation that is
induced during infection with C. rodentium causes changes in the composition of the gut
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microbiota that help to protect the host from the expansion and epithelial translocation of the
pathobiont Enterococcus faecalis79.

Another driver of changes in the nutritional environment of the gut is the generation of
reactive oxygen species and reactive nitrogen species during inflammation. Pro-
inflammatory cytokines such as interferon-γ (IFN-γ) activate dual oxidase 2 in the
intestinal epithelium, which produces hydrogen peroxide82. Increased expression of
DUOX2, the gene that encodes dual oxidase 2, in the intestinal mucosa of patients with
Crohn’s disease and ulcerative colitis correlates with an expansion of Proteobacteria in the
gut microbiota83. IFN-γ also induces epithelial expression of the gene Nos2 (ref. 84), which
encodes inducible nitric oxide synthase, the enzyme that catalyses the production of nitric
oxide from L-arginine85. As a result, the concentration of nitric oxide is elevated in gases
from the colons of people with inflammatory bowel disease86–88. Although reactive oxygen
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and nitrogen species have antimicrobial activity, these radicals quickly form non-toxic
compounds in the lumen of the gut as they diffuse away from the epithelium. For example,
when they are generated during inflammation by host enzymes in the intestinal epithelium,
these species react to form nitrate89. This by-product of inflammation is present at elevated
concentrations in the intestines of mice with chemically induced colitis90 (Fig. 3). Nitrate
reductases, enzymes that are broadly conserved among the Enterobacteriaceae, couple the
reduction of nitrate to energy-conserving electron transport systems for respiration, a process

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termed nitrate respiration. However, the genes that encode them are absent from the
genomes of obligate anaerobic Clostridia or Bacteroidia91. Nitrate respiration drives the
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Nos2-dependent expansion of commensal E. coli in mice with chemically or genetically

induced colitis, but not in animals without signs of intestinal inflammation91. Respiratory
electron acceptors that are generated as a by-product of the host inflammatory response
therefore create a niche in the lumen of the intestines that supports the uncontrolled
expansion of commensal Enterobacteriaceae rather than of obligate anaerobic bacteria91.
The resulting bloom in the inflamed intestine is one of the most consistent and robust
ecological patterns that has been observed in the gut microbiota92.

The creation of a niche for respiratory nutrients during inflammation is also an important
driver of the strategies that pathogenic bacteria from the family Enterobacteriaceae use to
invade the gut ecosystem. In the absence of inflammation or treatment with antibiotics,
members of the gut microbiota occupy all available nutrient niches, which makes it very
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challenging for pathogenic Enterobacteriaceae to enter the community. One solution is for
these bacteria to trigger intestinal inflammation, which would coerce the host into creating a
fresh niche of respiratory nutrients that is suitable for its expansion — an approach that is
used by S. Typhimurium93. On ingestion, S. Typhimurium uses T3SS-1 to invade the
intestinal epithelium94 and T3SS-2 to survive in the tissue of the host95. Both of these
processes trigger acute intestinal inflammation in cattle and in mouse models of
gastroenteritis96–98 (Fig. 3). The inflammatory response of the host drives the expansion of
S. Typhimurium in the lumen of the gut99, which is required for the transmission of this
pathogenic species to a new host through the faecal–oral route100.

Although such expansion allows S. Typhimurium to side-step competition with obligate

anaerobic Clostridia and Bacteroidia, this strategy forces the bacterium into battle with
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commensal Enterobacteriaceae over limited resources. For example, S. Typhimurium

expands in the inflamed gut through nitrate respiration101,102, which results in rivalry with
commensal Enterobacteriaceae that pursue a similar strategy91. S. Typhimurium can gain an
edge in this competition through its ability to utilize a broader range of inflammation-
derived electron acceptors than its rivals. A source of one such electron acceptor is sulfate-
reducing species of Desulfovibrio from the microbiota, which release hydrogen sulfide, a
compound that is converted to thiosulfate by the epithelium of the colon to avoid toxicity103.
Deployment of the virulence factors of pathogenic bacteria leads to the recruitment of
neutrophils to the intestinal mucosa, which is the histopathological hallmark of S.
Typhimurium-induced gastroenteritis96. A fraction of these recruited neutrophils migrate
into the lumen of the intestine — a diagnostic marker of inflammatory diarrhoea104. In the
lumen, neutrophils help to protect the mucosa by engulfing bacteria in the vicinity of the
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epithelium105, but reactive oxygen species that are generated by the phagocyte-produced
NADPH oxidase 2 (also known as cytochrome b-245 heavy chain) convert thiosulfate into
tetrathionate, a respiratory electron acceptor that supports the expansion of S. Typhimurium
in the lumen of the inflamed gut106 (Fig. 3). Although tetrathionate respiration is a
characteristic of Salmonella serovars and has been used empirically in their isolation in
clinical microbiology laboratories since 1923 (ref. 107), insights into the respiratory nutrient
niche that Salmonella occupies suggest that this property is part of a strategy to edge out
competing commensal Enterobacteriaceae in the inflamed gut106.

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The inflammatory response of the host also ignites competition between commensal and
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pathogenic Enterobacteriaceae over trace elements such as iron, which is less available
during inflammation. IL-22 induces the release of the antimicrobial protein lipocalin-2 (also
known as neutrophil gelatinase-associated lipocalin) from the epithelium in mice and rhesus
macaques108,109. Lipocalin-2 reduces iron availability by binding to enterobactin, a low-
molecular-weight iron chelator (or siderophore) that is produced by
Enterobacteriaceae110,111. To overcome this, S. Typhimurium and some commensal E. coli
secrete a glycosylated derivative of enterobactin, termed salmochelin, which is not bound by
lipocalin-2 (ref. 108). By producing salmochelin as well as two further siderophores that are
not bound by lipocalin-2, yersiniobactin and aerobactin, the probiotic E. coli strain Nissle
1917 can limit the expansion of S. Typhimurium in the lumen of the inflamed gut112.
Conversely, lipocalin-2 secretion by the epithelium generates an environment that enables S.
Typhimurium to edge out commensal Enterobacteriaceae that depend solely on enterobactin
for the acquisition of iron109 (Fig. 3).
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Through its limitation of iron availability, intestinal inflammation also sets the stage for
battles between Enterobacteriaceae that use protein-based toxins known as colicins113 that
affect a narrow range of hosts. Iron limitation induces the synthesis of siderophore receptor
proteins for the bacterial outer membrane113, which also commonly serve as receptors for
colicins114–116. Expression of a siderophore receptor protein termed the colicin I receptor
(CirA) confers commensal E. coli with sensitivity to colicin Ib produced by S.
Typhimurium113. The respiratory nutrient niche that is generated by the inflammatory
response of the host is therefore a battleground on which commensal and pathogenic
Enterobacteriaceae struggle for dominance using a diverse arsenal of nutritional and
antimicrobial strategies.
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Perspective and the future

The study of the microbiome began more than a century ago. equencing of 16S rRNA genes
provided the first insights into the taxonomic composition of microbial communities. Later,
sequencing of the complete metagenome of microbial communities provided a more detailed
insight into the full genetic capacity of such a community. The use of germ-free animals,
either alone or in combination with emerging technologies such as laser-capture
microdissection and transcriptomics, enabled mechanistic studies of the associations
between the microbiota, the host and pathogenic bacteria117. Multi-taxon insertion
sequencing now allows researchers to investigate both the assembly and the shared and
strain-specific dietary requirements of communities of microbes, and it has also facilitated
the informed manipulation of such communities through diet118. The development of
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quantitative imaging technologies has provided insight into the localization of microbes
within the gastrointestinal tract, and it has also enabled studies on the proximity of and
interactions between microbes119. The increasing refinement and power of metabolomics,
imaging mass spectrometry and three-dimensional mapping of mass-spectrometry data
provide a high-resolution image of the complex chemistry landscape of the interactions
between microbes and the host, which sets the stage for manipulating this chemistry to
prevent or treat infectious diseases24,38,120–127. A marriage of metagenomics and
mathematical modelling promises to enhance the precision of microbiome reconstitution,

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 Bäumler and Sperandio Page 11

which has proven successful for tackling C. difficile infections in mice128. In these exciting
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times, the expansion of multidisciplinary research is rapidly generating new technologies

and mechanistic insights into interactions between the microbiota, the host and pathogenic
bacteria (Box 1).

BOX 1

Microbiota interventions as therapeutic strategies to limit pathogen

expansion
An imbalance in the gut microbiota might underlie many human diseases but, in most
cases, the development of treatment options is still in its infancy. This could be in part
because the mechanisms that lead to adverse effects in the host differ for each disease,
which means that intervention strategies must be developed for each. The treatment
options for antibiotic-induced dysbiosis are perhaps the most advanced, mainly because
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faecal microbiota transplantation can reverse this imbalance in the gut microbiota129.
Nonetheless, the mechanisms through which treatment with antibiotics encourages an
uncontrolled expansion of the obligate anaerobe C. difficile differ markedly from those
that stimulate the growth of the facultative anaerobes Enterobacteriaceae, which has
implications for the development of precision microbiome interventions.

Mice that are treated with streptomycin have a reduced abundance of members of the
class Clostridia130, which are credited with producing the lion’s share of the short-chain
fatty acid butyrate in the large intestine131. The resulting depletion of short-chain fatty
acids drives an expansion of Enterobacteriaceae through mechanisms that are not fully
resolved44,132. Depletion of Clostridia-derived butyrate affects the metabolism of
enterocytes in the colon, which derive most of their energy by butyrate respiration133.
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The depletion of short-chain fatty acids also leads to a contraction in the pool of
regulatory T cells in the colonic mucosa134–136. These changes in the host physiology
increase the inflammatory tone of the mucosa, as indicated by the elevated expression of
Nos2, the gene that encodes inducible nitric oxide synthase, and contributes to the
expansion of commensal E. coli through nitrate generation137. Although other
mechanisms probably contribute to the post-antibiotic expansion of certain populations of
bacteria in the gut126, the transfer of Clostridia, with their capacity for producing short-
chain fatty acids, represents the most effective treatment for limiting the growth of E. coli
in streptomycin-treated mice138.

By contrast, the post-antibiotic expansion of the C. difficile population is driven by a

depletion of secondary bile salts. The liver produces the primary bile salts cholate and
chenodeoxycholate, which are conjugated to the amino acids taurine (to produce
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taurocholate and taurochenodeoxycholate) or glycine (to produce glycocholate and

glycochenodeoxycholate) and then secreted into the gut. Bile salt hydrolases, enzymes
that are produced by many members of the gut microbiota, remove the conjugated amino
acid from the primary bile salt. C. scindens is one of a limited number of species of
bacteria that can actively transport cholate and chenodeoxycholate into its cytosol, where
these unconjugated primary bile salts are converted into the secondary bile salts
deoxycholate and lithocholate, which are subsequently secreted into the extracellular

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 Bäumler and Sperandio Page 12

environment139 (Box Fig.). Although both primary and secondary bile salts induce the
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germination of C. difficile spores, only secondary bile salts efficiently prevent the growth
of vegetative C. difficile cells140. By significantly reducing the abundance of species that
are capable of producing deoxycholate and lithocholate, treatment with antibiotics causes
a depletion of these secondary bile salts and promotes the expansion of vegetative C.
difficile cells in the large intestine141,142. Faecal microbiota transplantation restores the
production of secondary bile salts and therefore prevents the expansion of C. difficile143.
Direct supplementation of the diet with secondary bile salts warrants caution because
increased concentrations of bile salts have been linked to gastrointestinal cancers144.
However, inoculation with only the secondary-bile-salt-producing C. scindens confers
mice with resistance to C. difficile expansion following treatment with antibiotics128.
This remarkable observation opens the door to novel precision microbiome interventions
that aim to prevent or treat the colitis that is associated with C. difficile infection after
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antibiotic therapy.
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Acknowledgments
Work in the V.S. laboratory is supported by US National Institutes of Health (NIH) grants AI053067, AI077613,
AI05135 and AI114511. Work in the A.J.B. laboratory is supported by US Department of Agriculture grant
Author Manuscript

2015-67015-22930 and NIH grants AI044170, AI096528, AI112445, AI114922 and AI117940. The contents of this
Review are solely the responsibility of the authors and do not necessarily represent the official views of the NIH
National Institute of Allergy and Infectious Diseases.

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Figure 1. The impact of antibiotics on the microbiota and the expansion of enteric pathogens
a, A diverse and non-disturbed microbiota confers resistance to colonization by enteric
pathogens in the intestinal epithelium. b, Treatment with antibiotics decreases the diversity
of the microbiota and leads to expansion of the C. difficile population. Toxins that are
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released from C. difficile (TcdA and TcdB) enter and damage the cells of the epithelium,
which leads to inflammation (colitis) and cell death. c, Treatment with antibiotics also leads
to an increase in the levels of free sialic acid (from the host) and succinate (from the
microbiota) in the lumen of the intestine. Elevated sialic acid promotes the expansion of the
S. Typhimurium population, which can lead to inflammation (gastroenteritis) if the
bacterium invades the cells of the intestinal epithelium. Elevated levels of sialic acid and
succinate further promote the expansion of the C. difficile population and the development
of colitis and cell death.

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Figure 2. Modulation of enterohaemorrhagic E. coli virulence through nutrients provided by the

microbiota
a, The microbiota resides in the lumen and outer mucus layer of the intestine. The
saccharolytic bacterium Bacteroides thetaiotaomicron is a prominent member of the
microbiota. It can release fucose from the mucus and makes the sugar available to other
bacteria. When EHEC senses fucose through the FusKR signalling system, it represses both
its use of the sugar and the expression of genes that encode the T3SS, a protein-translocation
apparatus that enables the bacterium to secrete effector proteins into host cells. This
repression prevents EHEC from competing for fucose with commensal E. coli and from
expending energy unnecessarily on T3SS expression. b, Metabolites that are provided by B.
thetaiotaomicron, such as succinate, lead to an increase in the expression by EHEC of the
enzyme mucinase, which obliterates the mucus layers of the intestine. EHEC is then able to
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reach the intestinal epithelium. B. thetaiotaomicron then begins to secrete succinate and
other metabolites that are required for gluconeogenesis into the now nutrient-poor
environment. The compounds are sensed by EHEC, which upregulates its expression of the
T3SS to enable the bacterium to attach to the epithelial cells of the host intestine and form
lesions that cause diarrhoea.
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Figure 3. The effect of intestinal inflammation on nutrient availability

S. Typhimurium uses its virulence factors (T3SS-1 and T3SS-2) to trigger intestinal
inflammation. Cytokines that are released during inflammation, such as IL-22 and IFN-γ,
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trigger the release of antimicrobial molecules lipocalin-2, reactive oxygen species (ROS) and
reactive nitrogen species (RNS) from the intestinal epithelium. Lipocalin-2 can block the
growth of commensal Enterobacteriaceae that rely on the siderophore enterobactin for the
acquisition of iron (Fe3+). It does not bind to the S. Typhimurium siderophone salmochelin,
however, which confers the bacterium with resistance to its effects on growth. RNS and ROS
react to form nitrate, which drives the growth of Enterobacteriaceae through nitrate
respiration. Microbiota-derived hydrogen sulfide is converted to thiosulfate by colonic
epithelial cells. Neutrophils that migrate into the lumen of the intestine during inflammation
generate ROS that convert endogenous sulfur compounds (thiosulfate) into an electron
acceptor (tetrathionate) that further boosts the growth of S. Typhimurium through
tetrathionate respiration.
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Nature. Author manuscript; available in PMC 2016 November 18.